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A semiempirical free energy force field with charge-based desolvation

✍ Scribed by Ruth Huey; Garrett M. Morris; Arthur J. Olson; David S. Goodsell

Publisher: John Wiley and Sons
Year: 2007
Tongue: English
Weight: 263 KB
Volume: 28
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.20634

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✦ Synopsis

Abstract

The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid‐based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge‐based method for evaluation of desolvation designed to use a typical set of atom types. The method has been calibrated on a set of 188 diverse protein–ligand complexes of known structure and binding energy, and tested on a set of 100 complexes of ligands with retroviral proteases. The force field shows improvement in redocking simulations over the previous AutoDock3 force field. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

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